Comprehensive AAV capsid fitness landscape reveals a viral gene and enables machine-guided design
Ontology highlight
ABSTRACT:
ORGANISM(S): Adeno-associated virus
PROVIDER: GSE139657 | GEO | 2019/11/29
REPOSITORIES: GEO
Similar Datasets
Project description: Not available
| S-EPMC7197022 | biostudies-literature
Project description:Comprehensive AAV capsid fitness landscape reveals a viral gene and enables machine-guided design
| PRJNA586835 | ENA
Project description:Recombinant adeno-associated viral vectors (rAAVs) are among the most commonly used vehicles for in vivo based gene therapies. However, it is hard to predict which AAV capsid will provide the most robust expression in human subjects due to the observed discordance in vector-mediated transduction between species. We used a primate specific capsid, AAV-LK03, and demonstrated that the limitation of this capsid towards transduction of mouse cells was unrelated to cell entry and nuclear transport but rather due to depleted histone H3 chemical modifications related to active transcription, namely H3K4me3 and H3K27ac, on the vector DNA itself. A single-amino acid insertion into the AAV-LK03 capsid enabled efficient transduction and the accumulation of active-related epigenetic marks on the vector chromatin in mouse without compromising transduction efficiency in human cells. Our study suggests that the capsid protein itself is involved in driving the epigenetic status of the vector genome, most likely during the process of uncoating. Programming viral chromatin states by capsid design may enable facile DNA transduction between vector and host species and ultimately led to rationale selection of AAV capsids for use in humans.
2023-02-28 | GSE226167 | GEO
Project description:Recombinant adeno-associated viral vectors (rAAVs) are among the most commonly used vehicles for in vivo based gene therapies. However, it is hard to predict which AAV capsid will provide the most robust expression in human subjects due to the observed discordance in vector-mediated transduction between species. We used a primate specific capsid, AAV-LK03, and demonstrated that the limitation of this capsid towards transduction of mouse cells was unrelated to cell entry and nuclear transport but rather due to depleted histone H3 chemical modifications related to active transcription, namely H3K4me3 and H3K27ac, on the vector DNA itself. A single-amino acid insertion into the AAV-LK03 capsid enabled efficient transduction and the accumulation of active-related epigenetic marks on the vector chromatin in mouse without compromising transduction efficiency in human cells. Our study suggests that the capsid protein itself is involved in driving the epigenetic status of the vector genome, most likely during the process of uncoating. Programming viral chromatin states by capsid design may enable facile DNA transduction between vector and host species and ultimately led to rationale selection of AAV capsids for use in humans.
2023-02-28 | GSE226165 | GEO
Project description:Recombinant adeno-associated viral vectors (rAAVs) are among the most commonly used vehicles for in vivo based gene therapies. However, it is hard to predict which AAV capsid will provide the most robust expression in human subjects due to the observed discordance in vector-mediated transduction between species. We used a primate specific capsid, AAV-LK03, and demonstrated that the limitation of this capsid towards transduction of mouse cells was unrelated to cell entry and nuclear transport but rather due to depleted histone H3 chemical modifications related to active transcription, namely H3K4me3 and H3K27ac, on the vector DNA itself. A single-amino acid insertion into the AAV-LK03 capsid enabled efficient transduction and the accumulation of active-related epigenetic marks on the vector chromatin in mouse without compromising transduction efficiency in human cells. Our study suggests that the capsid protein itself is involved in driving the epigenetic status of the vector genome, most likely during the process of uncoating. Programming viral chromatin states by capsid design may enable facile DNA transduction between vector and host species and ultimately led to rationale selection of AAV capsids for use in humans.
2023-02-28 | GSE226164 | GEO
Project description:Recombinant adeno-associated viral vectors (rAAVs) are among the most commonly used vehicles for in vivo based gene therapies. However, it is hard to predict which AAV capsid will provide the most robust expression in human subjects due to the observed discordance in vector-mediated transduction between species. We used a primate specific capsid, AAV-LK03, and demonstrated that the limitation of this capsid towards transduction of mouse cells was unrelated to cell entry and nuclear transport but rather due to depleted histone H3 chemical modifications related to active transcription, namely H3K4me3 and H3K27ac, on the vector DNA itself. A single-amino acid insertion into the AAV-LK03 capsid enabled efficient transduction and the accumulation of active-related epigenetic marks on the vector chromatin in mouse without compromising transduction efficiency in human cells. Our study suggests that the capsid protein itself is involved in driving the epigenetic status of the vector genome, most likely during the process of uncoating. Programming viral chromatin states by capsid design may enable facile DNA transduction between vector and host species and ultimately led to rationale selection of AAV capsids for use in humans.
2023-02-28 | GSE226264 | GEO
Project description:Cell-mediated immune (CMI) responses to adeno-associated virus (AAV) can lead to both tissue damage and loss of therapeutic transgene expression. Identifying robust biomarkers of CMI and understanding CMI mechanisms can be help to helpful in clinical practice and in advancement of AAV gene therapies. The present work evaluated PBMCs from non-human primates (NHP) before and 14 days following immunization with AAV9 capsid. PBMCs were stimulated in vitro with AA9 capsid peptides to evaluate CMI responses by IFN- ELISPOT, intracellular cytokines and activation markers by flow cytometry, secreted cytokines by ELISAMSD, and transcriptional responses by RNAseq. AAV peptide stimulation produced a robust IFN- ELISPOT response at 14 days. Flow cytometry revealed an increase in IFN- positive CD4 and CD8 cells, IL2 positive CD4 cells, and TNF positive CD4 cells. An increase in the CXCR3 ligands IP-10 and I-TAC were detected both inas secreted proteins. The most robust changes in response to AAV stimulation and strongest correlations to ELISPOT response were revealed by RNAseq, including transcripts encoding IFN- and transcripts encoding , IP-10 and I-TAC , and many downstream transcripts and several IFN-independent pathways. These data provide evidence that a gene signature, or CXCR3 ligand transcripts or protein could serve as robust and sensitive alternatives to ELISPOT for detection of CMI, andCMI and warrant further benchmarking in human samples.
2024-02-26 | GSE256418 | GEO
Project description:Brief assessment of VEEV TC-83 Capsid:RNA interactions.
2020-05-25 | GSE132125 | GEO
Project description:Adeno-associated virus (AAV) has emerged as a leading platform for gene therapy. With a skyrocketing rate of AAV research and the prevalence of many new engineered capsids being investigated in preclinical and clinical trials, capsid characterization plays an important role in serotype confirmation and quality control. Further, peptide mapping the capsid proteins might inevitably be a future requirement by regulatory agencies since it is a critical step in good manufacturing practice (GMP) for biotherapeutic characterization. To overcome many challenges that traditional methods like SDS-PAGE and Western blots carry, liquid chromatography & mass spectrometry (LC-MS) allows high resolution & sensitivity with great confidence in characterizing the AAV capsid proteins to the exact masses. Our optimized LC-MS method provides quick sample preparation, fast and high-throughput 4-min run, high sensitivity (only need ~2E10 vg per run for UV detection) allowing very efficient characterization of wild-type and engineered capsids. Additionally, , as well as LC-MS/MS peptide mapping of the AAV capsid proteins, including. lLysine-targeted chemical modification of the AAV capsids, for the first time, was characterized and peptide mapped in this study, therefore elucidating the most accessible Lysine residues of the AAV tested. Our detailed protocols method areis anticipated to promote the development and discovery of AAV variants with high accuracy and efficiency.
2023-03-11 | PXD035837 | Pride
Project description:The hepatitis E virus (HEV), a non enveloped RNA virus, causes viral hepatitis. The viral open reading frame 2 (ORF2) protein represents the capsid protein of HEV which is known to cause endoplasmic reticulum stress in ORF2 expressing cells. The initiation of endoplasmic reticulum stress induced apoptosis mainly involves the transcriptional activation of pro-apoptotic gene CHOP which will further trigger the major apoptotic pathways. However, the activation of CHOP by ORF2 protein in this study does not induce apoptotic markers such as Bax translocation to mitochondria. We have used the Affymetrix microarray platform to screen the pro-apoptotic effects induced by the expression of ORF2 protein in human hepatic cell lines (Huh7). The Huh7 cells were transduced either with recombinant adenovirus encoding the HEV ORF2 (Ad-ORF2) or an adenovirus encoding the green fluorescent protein (Ad-GFP). The array results consistently showed an ORF2 specific induction of mRNA corresponding to the chaperones Hsp72, Hsp70B’ and co-chaperone Hsp40. These studies provide further mechanisms of the ER stress mediated pro apoptotic effects caused by the ORF2 protein and its potential role for the activation of anti-apoptotic activity of the host cell. We used microarray to screen the host genes were regulated by the expression of the hepatitis E virus capsid protein. Huh7 cells transduced with Ad-GFP (control) or with Ad-HEV ORF2.
2012-12-01 | E-GEOD-29061 | biostudies-arrayexpress